Yes, moisture will collect. I had to change a dust seal I put in wrong on a caliper, and when I took it apart, there was a little bit of water in the piston area. I had them sleeved with stailess, so no damage, but I gave both sides a good flush anyway. My system was all new also.

A trick I was taught was to place the container of DOT 5 fluid in a pan of boiling water. Makes the small suspended air bubles expand and rise to the top. The fact that it doesn't eat paint away is the biggest reason I use it.